Introducing a simple model system for binding studies of known and novel inhibitors of AMPK: a therapeutic target for prostate cancer

Prostate cancer (PC) is one of the leading cancers in men, raising a serious health issue worldwide. Due to lack of suitable biomarker, their inhibitors and the platform for testing those inhibitors result in poor prognosis of PC. AMP-activated protein kinase (AMPK) is a highly conserved protein kinase found in eukaryotes that is involved in growth and development, and also acts as a therapeutic target for PC. The aim of the present study is to identify novel potent inhibitors of AMPK and propose a simple cellular model system for understanding its biology. Structural modelling and MD simulations were performed to construct and refine the 3D models of Dictyostelium and human AMPK. Binding mechanisms of different drug compounds were studied by performing molecular docking, molecular dynamics and MM-PBSA methods. Two novel drugs were isolated having higher binding affinity over the known drugs and hydrophobic forces that played a key role during protein–ligand interactions. The study also explored the simple cellular model system for drug screening and understanding the biology of a therapeutic target by performing in vitro experiments.     

Evaluation of fungicides to control potato late blight (Phytophthora infestans) in the plains of Nepal

Fungicide application is an effective management option to control late blight of potato (caused by Phytophthora infestans). Field experiments were conducted to evaluate the efficacy of recently introduced and previously used fungicides on late blight management and potato yields in the western plains of Nepal in 2015 and 2016 crop seasons. Fungicides and a non-treated control (NTC) were replicated three times in a randomized block design planted with late blight susceptible cultivar Cardinal. Chlorothalonil, copper oxychloride, dimethomorph, fenamidone + mancozeb, mancozeb and metalaxyl were sprayed in 2015. In 2016, carbendazim was used instead of chlorothalonil. The area under disease progress curve (AUDPC) was consistently reduced in years by dimethomorph (90% and 65% in 2015 and 2016, respectively), fenamidone + mancozeb (68% and 62%) and mancozeb (40% and 47%) compared with the NTC. Similarly, tuber yield was increased with the application of dimethomorph (266% and 146% in 2015 and 2016, respectively), fenamidone + mancozeb (211% and 155%) and mancozeb (136% and 116%) compared with the NTC. Chlorothalonil reduced AUDPC by 43% and increased tuber yield by 170% in 2015. Other fungicides either had inconsistent results or did not reduce late blight severity and consequent effects on potato yield. The overall benefit–cost ratio was highest for dimethomorph in both years. These results show efficacy of dimethomorph, fenamidone + mancozeb and mancozeb in reducing late blight severity and increasing potato tuber yield in the plains of Nepal.     

Resuscitation Promoting Factors: a Family of Microbial Proteins in Survival and Resuscitation of Dormant Mycobacteria

Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is an extraordinarily successful pathogen of humankind. It has been estimated that up to one-third of the world’s population is infected with M. tuberculosis, and this population is an important reservoir for disease reactivation. Resuscitation promoting factor (Rpf) is a secretory protein, which was first reported in Micrococcus luteus. There are five functionally redundant Rpf-like proteins found in M. tuberculosis. Rpf promotes the resuscitation of dormant bacilli to yield normal, viable colony forming bacteria. All Rpfs share a conserved domain of about 70 amino acids and possess a lysozyme-like activity. The structural studies of the conserved domain suggest that Rpfs could be considered as a c-type lysozyme and lytic transglycosylases. Recently a novel class of nitrophenylthiocyanates (NPT) inhibitors of the muralytic activity of Rpf were reported which opens a new approach in the study of cell-wall hydrolyzing enzymes. This review describes molecular and structural studies conducted on Rpf proteins, their role in the resuscitation of dormant bacteria, in the reactivation of latent infection and identification of low molecular weight inhibitors of resuscitation promoting factors.     

In silico modeling of ligand molecule for non structural 3 (NS3) protein target of flaviviruses

Flaviviruses are small, enveloped RNA viruses which cause a variety of diseases into animals and man. Despite the existence of licensed vaccines, yellow fever, Japanese encephalitis and tick-borne encephalitis also claim many thousands of victims each year across their vast endemic areas. A number of studies have already revealed that the non-structural NS3 serine protease is required for the maturation of the viral polyprotein and thus is a promising target for the development of antiviral inhibitors. Hence, the 3D structure of NS3 protein was modeled using homology modeling by MODELLER 9v7. Validation of the constructed NS3 protein models were done by PROCHECK, VERYFY3D and through ProSA calculations. Ligands for the catalytic triad (H51, D75, and S135) were designed using LIGBUILDER. The NS3 protein's catalytic triad was explored to find out the interactions pattern for inhibitor binding using molecular docking methodology using AUTODOCK Vina. The interactions of complex NS3protein-ligand conformations, including hydrogen bonds and the bond lengths were analyzed using Accelrys DS Visualizer software. Hence, from this observation, the novel molecule designed was observed to be the best ligand against the NS3 protein of flavivirus. This molecule may prove to be a potential identity in modulating disease manifestation for all the selected flavivirus members. ABBREVIATIONS: NCBI - National Centre for Biotechnological Information, BLAST - Basic Local Alignment Search Tool, DOPE - Discrete optimized protein energy, GROMOS96 - GROningen MOlecular Simulation package, SAVS - Structure Analysis and Validation Server.     

Higher acyclic nitrogen containing deoxy sugar derivatives: a new lead in the generation of antimycobacterial chemotherapeutics

Syntheses of higher acyclic nitrogen containing deoxy sugar derivatives via nitroaldol reaction of different nitroalkanes with 2,3-dideoxy-alpha,beta-unsaturated aldehydo sugars obtained from glycals namely acetylated glucal and galactal and their in vitro antimycobacterial activity are presented.     

Experiments and three phase modelling of a biofilter for the removal of toluene and trichloroethylene

Volatile organic compounds, namely, toluene, trichloroethylene, styrene, etc., disposed off by electronics and polymer industries, are very harmful. The treatment of VOC laden air through biochemical route is one of the potential options for reduction of their concentration in parts per million or parts per billion level. Under the present investigation, a 0.05-m diameter and 0.58-m high trickle bed biofilter has been studied for the removal of VOCs namely toluene and trichloroethylene from a simulated air–VOC mixture using pure strain of Pseudomonas putida (NCIM2650) in immobilized form. Inlet concentrations of VOCs have been varied in two ranges, the lower being 0.20–2.00 g/m³ and higher being 10–20 g/m³, respectively. The Monod type rate kinetics of removal of VOCs has been determined. A three-phase deterministic mathematical model has been developed taking the simultaneous reaction kinetics and interphase (gas to liquid to biofilm) mass transfer rate of VOCs into consideration. Experimentally determined kinetic parameters and mass transfer coefficients calculated using standard correlations have been used. Concentrations have been simulated for all the three phases. Simulated results based on the model have been compared with the experimental ones for both gas and liquid phases satisfactorily. The mathematical model validated through the successful comparison with experimental data may be utilized for the prediction of performance of biofilters undergoing removal of different VOCs in any further investigation and may be utilized for the scale-up of the system to industrial scale.     

Poly-3-hydroxyoctanoate P(3HO), a medium chain length polyhydroxyalkanoate homopolymer from Pseudomonas mendocina

Pseudomonas mendocina was found to produce a unique homopolymer of poly(3-hydroxyoctanoate), P(3HO), rather than a copolymer, when grown on sodium octanoate as the sole carbon source. Although this polymer has been produced by other organisms, interestingly this is the first time an absolute homopolymer has been produced by a wild type organism. In addition, a detailed study on the effects of different extraction methods on the yield, molecular weight, thermal properties, and lipopolysaccharide content of P(3HO) has been carried out. The organism was able to accumulate P(3HO) up to 31.38% of its dry cell weight within 48 h in mineral salt medium. Characterization of the monomer was carried out using FTIR, GC-MS, (13)C, (1)H, and HSQC NMR spectroscopy. The polymer had a crystallinity of 37.5%, Young's modulus value of 11.6 MPa and contact angle of 77.3°. Microstructural studies of solvent cast polymer films revealed a smooth surface topography with a root-mean-square roughness value of 0.238 μm.